EP Toolkit version 2.41 has been released:
https://sourceforge.net/projects/erppcatoolkit/
Aside from the usual bug fixes and refinements, notable upgrades include the addition of MRI artifact correction routines to preprocessing, a fix for the font sizes on Windows computers, and a segmentation function. A notable bug fix was for the robust ANOVA function for between-group analyses. My usual practice is to sort the between group identifier column alphabetically. It turned out that when it was not sorted alphabetically, the subjects were not being assigned to the correct group, usually resulting in null effects. My apologies for this bug. I’m continuing to work with EGI to improve the support for mff files but they are still a work in progress. Please read the notes at the end of this list if you are an OS X user.
**I’d also like to note that I am interested in opportunities for collaborating on grant submissions.**
Changes include:
1) When saving simple binary files with events, fractional sample durations rounded up.
2) Dropped setting bad one second epochs to 1000µv when saving simple binary continuous files.
3) Fixed crash when reading file with TRSP events that was not in mff format.
4) Fixed crash when translating single-trial EP file to EEGlab format and there are no events.
5) "boundary" in .type as well as .value fields for boundary events.
6) Added .keys field to events field to hold additional information, especially for mff files.
7) Added subject specs support for mff files.
8) Fixed EEGlab .set files not including study name in file name.
9) Fixes font sizes on Windows.
10) Fixed “About EP Toolkit” spawning new main window.
11) Fixed not checking to see if file name already exists when saving an EEGLab .study file.
12) For continuous data in Waves and Scan functions, baseline correct each channel by entire one second epoch so that waves will be visible.
13) + and - change scale buttons added to Scan function.
14) Scan and Waves functions can now present event markings.
14) Fixed crash in view waves function when superimposing two datasets where one is missing channel coordinates
15) When channel type is changed using Edit function to REG, ANS, or ECG, electrode coordinates are set to missing.
16) Added Segment Data function.
17) Filtering will not cross boundaries.
18) .analysis edit fields updated when points dropped from a continuous file. Boundary events added as needed.
19) Added fMRI artifact correction option to Preprocess data function
20) Fixed crash in blink correction when there is more than one bad channel.
21) Adds blink artifact channel and event marking peak latency of the blink in each epoch.
22) Blink correction checks for semi-singular data matrix, as from bridged channels, and drops dimensions as needed to improve quality of solution.
23) Averaging keeps all the events from the averaged data.
23) Adds saccade artifact channel and event marking onset latency of the saccade in each epoch.
24) In Scan function, added toggle to center data and a toggle to switch between clicking to mark bad channels and clicking to expand the waveform into a separate window.
25) Fixed frequency domain transform of continuous data not generating proper recTime field, resulting in later crashes.
26) Fixed crash in Topos function when trying to change scaling of frequency-domain data.
27) Preprocessing does not write over existing files.
28) Fixed noise and std fields set same as the data when combining cells or subjects.
29) Fixed crashes in preprocessing when there are multiple bad channels.
30) Fixed in Edit function added new subject or cell duplicating existing name resulted in corrupted file.
31) Fixed crash when regenerating cache and there is a spatial PCA in the active set.
32) Added windowing function option to window 'all' the channels.
33) Fixed crash in Preprocessing when there are multiple global and trialwise bad channels when running under a version of Matlab earlier than 2013a.
34) Fixed crash when reading .set files using single file mode.
35) Fixed between group ANOVAs not being calculated correctly when the between group variable is not sorted alphabetically.
36) Fixed crash in Edit function when adding factors together.
37) Fixed crashes in Template function when there is a non EEG channel present.
38) Fixed crash in Template function when switching between datasets with different electrode montages or epoch length.
39) Fixed crash introduced in 2.40 when performing two-step PCA.
I’ve also committed changes to the FieldTrip I/O to allow user-added custom EEGlab event fields to be read so the FieldTrip copy should be updated to 11/1/13 or later. Also, when I upgraded to OS X 10.9 (Mavericks), I started getting a lot of momentary freezing of the Matlab user interface. It appears that a number of third-party packages are incompatible. My own issues were solved using the Console utility, which identified RSSbot as having an endless stream of error messages, and the Activity Monitor utility, which identified Safari as having a lot of hung subprocesses, which I in turn tracked to the Flash Player plugin. Also, upgrading XQuartz to 2.75 (which the Mavericks installer does not do for you) made a big difference for Matlab specifically.
--------------------------------------------------------------------------------
Joseph Dien,
Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland
E-mail: jdien07@...
http://joedien.com

Oops! I’ll have a fix out to you tomorrow. I’m in the final stages of posting a new release and will include the fix as part of it. Thanks for the report!
Joe
On Dec 28, 2013, at 4:33 AM, Maria Serena Panasiti <m.serenapanasiti@...> wrote:
> Dear Joe,
>
> it worked perfectly, thank you very much. Unfurtunaltely I am having a new problem: I run the first step temporal PCA and everything goes fine, when I then try to run the spatial pca on the temporal PCA factors I get this error:
>
> ??? Reference to non-existent field 'recTime'.
>
> Error in ==> ep_doPCA at 879
> FactorResults.recTime=theData.recTime;
>
> Error in ==> ep_doPCAst at 339
> [stFactorResults] = ep_doPCA('asis', ROTATION, ROTOPT, MAT_TYPE, NUM_FAC, theData, LOADING);
>
> Error in ==> ep>pickPCAdata at 5593
> FactorResults = ep_doPCAst(theData.pca, 'UNRT', EPmain.pca.rotopt, PCArel, 1, PCAloading,PCAmode); %scree test only
> needs unrotated solution
>
> ??? Error while evaluating uicontrol Callback
>
>
> If I put a comment before this part of the ep_doPCA script:
>
> %FactorResults.recTime=theData.recTime;
>
> then the the scree test works, and the spatial PCA (Infomax rotation) actually starts but at the very end I get this error:
>
> Done with reconstructing PCA waveforms...
> ??? Index exceeds matrix dimensions.
>
> Error in ==> ep_addToEPworkCache at 123
> minFac=min(min(min(EPdata.data(EEGchans,:,theCell,theSub,theFactor,:))));
>
> Error in ==> ep_saveEPdataset at 75
> newDataset=ep_addToEPworkCache(EPdata);
>
> Error in ==> ep>pickPCAdata at 5730
> EPdataset=ep_saveEPdataset(EPdataset,PCAoutput,length(EPdataset.dataset)+1,'no');
>
> ??? Error while evaluating uicontrol Callback
>
> The same thing happens if i try to run the spatial PCA on the average data.
>
> I am using Matlab 2007b but I have also try Matlab 2011
> Eeglab 8_3
> Fieldtrip lite last version available
>
> I thank you in advance for your help and apologize if the question is too basic, I've tried to solve the problem by reading the tutorial but I couldn't figure it out.
>
> Best wishes,
>
> Serena
>
>
>
> On 15 December 2013 07:51, Joseph Dien <jdien07@...> wrote:
> I’m going to assume that you are using a file format like Neuroscan .AVG where each condition of each subject is a separate file. If so, use the Single File option of the Read function to import them (see documentation). It’ll form a single file in which each subject and each condition is separate but are all held in a single file for convenience sake.
>
> Cheers!
>
> Joe
>
>
> On Dec 14, 2013, at 4:56 AM, Maria Serena Panasiti <m.serenapanasiti@...> wrote:
>
>> Dear All,
>>
>> I have just downloaded the toolkit to perform PCA on my averaged data. I am struggling to understand how I can keep my experimental conditions separeted when I read my data on the toolkit.
>>
>> I have two experimental conditions for each subject. I glued all of the averages together in the edit window (append function); I gave the same subject name to the two experimental conditions averages and assigned them a weight of :
>>
>> weight name
>> 1 sub001 (This would be: AVg condtion1 subject1)
>> 1 sub001 (This would be: AVg condtion2 subject1)
>> 1 sub002 (This would be: AVg condtion1 subject2)
>> 1 sub002 (This would be: AVg condtion2 subject2)
>> 1 sub003 (This would be: AVg condtion1 subject3)
>> 1 sub003 (This would be: AVg condtion2 subject3)
>>
>>
>>
>> When I run the PCA, the toolkit treats each raw as a single participant (in the command window it would count up to six in this case)
>> So I was wondering if this was the right way to feed the program with different averages per conditions.
>>
>> As I understood PCA I should need to keep conditions separated but please tell me if I am wrong.
>>
>> Any help would be very much appreciated.
>>
>> Best wishes,
>>
>> Serena
>>
>>
>>
>> --
>> Maria Serena Panasiti, Ph.D
>>
>> Cognitive Social and Affective Neuroscience Lab
>> Department of Psychology.
>> University of Rome "La Sapienza".
>> Via dei Marsi 78 - 00185 - Roma.
>> Phone: (+39) 06-49917635. Fax: (+39) 06-49917635
>>
>> School of Psychology & Clinical Language Sciences
>> University of Reading
>> Reading, United Kingdom
>>
>> ------------------------------------------------------------------------------
>> Rapidly troubleshoot problems before they affect your business. Most IT
>> organizations don't have a clear picture of how application performance
>> affects their revenue. With AppDynamics, you get 100% visibility into your
>> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
>> http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk_______________________________________________
>> Erppcatoolkit-support mailing list
>> Erppcatoolkit-support@...
>> https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support
>
>
> --------------------------------------------------------------------------------
>
> Joseph Dien,
> Senior Research Scientist
> Maryland Neuroimaging Center
> University of Maryland
>
> E-mail: jdien07@...
> Phone: 202-297-8117
> http://joedien.com
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> --
> Maria Serena Panasiti, Ph.D
>
> Cognitive Social and Affective Neuroscience Lab
> Department of Psychology.
> University of Rome "La Sapienza".
> Via dei Marsi 78 - 00185 - Roma.
> Phone: (+39) 06-49917635. Fax: (+39) 06-49917635
>
> School of Psychology & Clinical Language Sciences
> University of Reading
> Reading, United Kingdom

*Dear Joe,*
*it worked perfectly, thank you very much. Unfurtunaltely I am having a new
problem: I run the first step temporal PCA and everything goes fine, when I
then try to run the spatial pca on the temporal PCA factors I get this
error:*
??? Reference to non-existent field 'recTime'.
Error in ==> ep_doPCA at 879
FactorResults.recTime=theData.recTime;
Error in ==> ep_doPCAst at 339
[stFactorResults] = ep_doPCA('asis', ROTATION, ROTOPT, MAT_TYPE,
NUM_FAC, theData, LOADING);
Error in ==> ep>pickPCAdata at 5593
FactorResults = ep_doPCAst(theData.pca, 'UNRT', EPmain.pca.rotopt,
PCArel, 1, PCAloading,PCAmode); %scree test only
needs unrotated solution
??? Error while evaluating uicontrol Callback
*If I put a comment before this part of the ep_doPCA script:*
%FactorResults.recTime=theData.recTime;
*then the the scree test works, and the spatial PCA (Infomax rotation)
actually starts but at the very end I get this error:*
Done with reconstructing PCA waveforms...
??? Index exceeds matrix dimensions.
Error in ==> ep_addToEPworkCache at 123
minFac=min(min(min(EPdata.data(EEGchans,:,theCell,theSub,theFactor,:))));
Error in ==> ep_saveEPdataset at 75
newDataset=ep_addToEPworkCache(EPdata);
Error in ==> ep>pickPCAdata at 5730
EPdataset=ep_saveEPdataset(EPdataset,PCAoutput,length(EPdataset.dataset)+1,'no');
??? Error while evaluating uicontrol Callback
*The same thing happens if i try to run the spatial PCA on the average
data.*
*I am using Matlab 2007b but I have also try Matlab 2011*
* Eeglab 8_3*
* Fieldtrip lite last version available*
*I thank you in advance for your help and apologize if the question is too
basic, I've tried to solve the problem by reading the tutorial but I
couldn't figure it out.*
*Best wishes,*
*Serena*
On 15 December 2013 07:51, Joseph Dien <jdien07@...> wrote:
> I’m going to assume that you are using a file format like Neuroscan .AVG
> where each condition of each subject is a separate file. If so, use the
> Single File option of the Read function to import them (see documentation).
> It’ll form a single file in which each subject and each condition is
> separate but are all held in a single file for convenience sake.
>
> Cheers!
>
> Joe
>
>
> On Dec 14, 2013, at 4:56 AM, Maria Serena Panasiti <
> m.serenapanasiti@...> wrote:
>
> Dear All,
>
> I have just downloaded the toolkit to perform PCA on my averaged data. I
> am struggling to understand how I can keep my experimental conditions
> separeted when I read my data on the toolkit.
>
> I have two experimental conditions for each subject. I glued all of the
> averages together in the edit window (append function); I gave the same
> subject name to the two experimental conditions averages and assigned them
> a weight of :
>
> weight name
> 1 sub001 (This would be: AVg condtion1 subject1)
> 1 sub001 (This would be: AVg condtion2 subject1)
> 1 sub002 (This would be: AVg condtion1 subject2)
> 1 sub002 (This would be: AVg condtion2 subject2)
> 1 sub003 (This would be: AVg condtion1 subject3)
> 1 sub003 (This would be: AVg condtion2 subject3)
>
>
>
> When I run the PCA, the toolkit treats each raw as a single participant
> (in the command window it would count up to six in this case)
> So I was wondering if this was the right way to feed the program with
> different averages per conditions.
>
> As I understood PCA I should need to keep conditions separated but please
> tell me if I am wrong.
>
> Any help would be very much appreciated.
>
> Best wishes,
>
> Serena
>
>
>
> --
> Maria Serena Panasiti, Ph.D
>
> Cognitive Social and Affective Neuroscience Lab
> Department of Psychology.
> University of Rome "La Sapienza".
> Via dei Marsi 78 - 00185 - Roma.
> Phone: (+39) 06-49917635. Fax: (+39) 06-49917635
>
> School of Psychology & Clinical Language Sciences
> University of Reading
> Reading, United Kingdom
>
> ------------------------------------------------------------------------------
> Rapidly troubleshoot problems before they affect your business. Most IT
> organizations don't have a clear picture of how application performance
> affects their revenue. With AppDynamics, you get 100% visibility into your
> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics
> Pro!
>
> http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk_______________________________________________
> Erppcatoolkit-support mailing list
> Erppcatoolkit-support@...
> https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support
>
>
>
>
> --------------------------------------------------------------------------------
>
> Joseph Dien,
> Senior Research Scientist
> Maryland Neuroimaging Center
> University of Maryland
>
> E-mail: jdien07@...
> Phone: 202-297-8117
> http://joedien.com
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
--
Maria Serena Panasiti, Ph.D
Cognitive Social and Affective Neuroscience Lab
Department of Psychology.
University of Rome "La Sapienza".
Via dei Marsi 78 - 00185 - Roma.
Phone: (+39) 06-49917635. Fax: (+39) 06-49917635
School of Psychology & Clinical Language Sciences
University of Reading
Reading, United Kingdom

I’m going to assume that you are using a file format like Neuroscan .AVG where each condition of each subject is a separate file. If so, use the Single File option of the Read function to import them (see documentation). It’ll form a single file in which each subject and each condition is separate but are all held in a single file for convenience sake.
Cheers!
Joe
On Dec 14, 2013, at 4:56 AM, Maria Serena Panasiti <m.serenapanasiti@...> wrote:
> Dear All,
>
> I have just downloaded the toolkit to perform PCA on my averaged data. I am struggling to understand how I can keep my experimental conditions separeted when I read my data on the toolkit.
>
> I have two experimental conditions for each subject. I glued all of the averages together in the edit window (append function); I gave the same subject name to the two experimental conditions averages and assigned them a weight of :
>
> weight name
> 1 sub001 (This would be: AVg condtion1 subject1)
> 1 sub001 (This would be: AVg condtion2 subject1)
> 1 sub002 (This would be: AVg condtion1 subject2)
> 1 sub002 (This would be: AVg condtion2 subject2)
> 1 sub003 (This would be: AVg condtion1 subject3)
> 1 sub003 (This would be: AVg condtion2 subject3)
>
>
>
> When I run the PCA, the toolkit treats each raw as a single participant (in the command window it would count up to six in this case)
> So I was wondering if this was the right way to feed the program with different averages per conditions.
>
> As I understood PCA I should need to keep conditions separated but please tell me if I am wrong.
>
> Any help would be very much appreciated.
>
> Best wishes,
>
> Serena
>
>
>
> --
> Maria Serena Panasiti, Ph.D
>
> Cognitive Social and Affective Neuroscience Lab
> Department of Psychology.
> University of Rome "La Sapienza".
> Via dei Marsi 78 - 00185 - Roma.
> Phone: (+39) 06-49917635. Fax: (+39) 06-49917635
>
> School of Psychology & Clinical Language Sciences
> University of Reading
> Reading, United Kingdom
>
> ------------------------------------------------------------------------------
> Rapidly troubleshoot problems before they affect your business. Most IT
> organizations don't have a clear picture of how application performance
> affects their revenue. With AppDynamics, you get 100% visibility into your
> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
> http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk_______________________________________________
> Erppcatoolkit-support mailing list
> Erppcatoolkit-support@...
> https://lists.sourceforge.net/lists/listinfo/erppcatoolkit-support
--------------------------------------------------------------------------------
Joseph Dien,
Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland
E-mail: jdien07@...
Phone: 202-297-8117
http://joedien.com

Dear All,
I have just downloaded the toolkit to perform PCA on my averaged data. I am
struggling to understand how I can keep my experimental conditions
separeted when I read my data on the toolkit.
I have two experimental conditions for each subject. I glued all of the
averages together in the edit window (append function); I gave the same
subject name to the two experimental conditions averages and assigned them
a weight of :
weight name
1 sub001 (This would be: AVg condtion1 subject1)
1 sub001 (This would be: AVg condtion2 subject1)
1 sub002 (This would be: AVg condtion1 subject2)
1 sub002 (This would be: AVg condtion2 subject2)
1 sub003 (This would be: AVg condtion1 subject3)
1 sub003 (This would be: AVg condtion2 subject3)
When I run the PCA, the toolkit treats each raw as a single participant (in
the command window it would count up to six in this case)
So I was wondering if this was the right way to feed the program with
different averages per conditions.
As I understood PCA I should need to keep conditions separated but please
tell me if I am wrong.
Any help would be very much appreciated.
Best wishes,
Serena
--
Maria Serena Panasiti, Ph.D
Cognitive Social and Affective Neuroscience Lab
Department of Psychology.
University of Rome "La Sapienza".
Via dei Marsi 78 - 00185 - Roma.
Phone: (+39) 06-49917635. Fax: (+39) 06-49917635
School of Psychology & Clinical Language Sciences
University of Reading
Reading, United Kingdom